7,503 research outputs found
Evolution of a fluorinated green fluorescent protein
The fluorescence of bacterial cells expressing a variant (GFPm) of the green fluorescent protein (GFP) was reduced to background levels by global replacement of the leucine residues of GFPm by 5,5,5-trifluoroleucine. Eleven rounds of random mutagenesis and screening via fluorescence-activated cell sorting yielded a GFP mutant containing 20 amino acid substitutions. The mutant protein in fluorinated form showed improved folding efficiency both in vivo and in vitro, and the median fluorescence of cells expressing the fluorinated protein was improved {approx}650-fold in comparison to that of cells expressing fluorinated GFPm. The success of this approach demonstrates the feasibility of engineering functional proteins containing many copies of abiological amino acid constituents
Probit models for capture-recapture data subject to imperfect detection, individual heterogeneity and misidentification
As noninvasive sampling techniques for animal populations have become more
popular, there has been increasing interest in the development of
capture-recapture models that can accommodate both imperfect detection and
misidentification of individuals (e.g., due to genotyping error). However,
current methods do not allow for individual variation in parameters, such as
detection or survival probability. Here we develop misidentification models for
capture-recapture data that can simultaneously account for temporal variation,
behavioral effects and individual heterogeneity in parameters. To facilitate
Bayesian inference using our approach, we extend standard probit regression
techniques to latent multinomial models where the dimension and zeros of the
response cannot be observed. We also present a novel Metropolis-Hastings within
Gibbs algorithm for fitting these models using Markov chain Monte Carlo. Using
closed population abundance models for illustration, we re-visit a DNA
capture-recapture population study of black bears in Michigan, USA and find
evidence of misidentification due to genotyping error, as well as temporal,
behavioral and individual variation in detection probability. We also estimate
a salamander population of known size from laboratory experiments evaluating
the effectiveness of a marking technique commonly used for amphibians and fish.
Our model was able to reliably estimate the size of this population and
provided evidence of individual heterogeneity in misidentification probability
that is attributable to variable mark quality. Our approach is more
computationally demanding than previously proposed methods, but it provides the
flexibility necessary for a much broader suite of models to be explored while
properly accounting for uncertainty introduced by misidentification and
imperfect detection. In the absence of misidentification, our probit
formulation also provides a convenient and efficient Gibbs sampler for Bayesian
analysis of traditional closed population capture-recapture data.Comment: Published in at http://dx.doi.org/10.1214/14-AOAS783 the Annals of
Applied Statistics (http://www.imstat.org/aoas/) by the Institute of
Mathematical Statistics (http://www.imstat.org
The Rwenzori Mountains, a Paleoproterzoic crustal shear belt crossing the Albertine rift system
This contribution discusses the development of the Paleoproterozoic Buganda-Toro belt in the Rwenzori mountains and its influence on the western part of the East African Rift System in Uganda. The Buganda-Toro belt is composed of several thick-skinned nappes consisting of Archaean Gneisses and Palaeoproterozoic cover units that are thrusted northwards. The high Rwenzori mountains are located in the frontal unit of this belt with retrograde greenschist facies gneisses towards the north, which are unconformably overlain by metasediments and amphibolites. Towards the south the metasediments are overthrust by the next migmatitic gneiss unit that belongs to a crustal scale nappe. The southwards dipping metasedimentary and volcanic sequence in the high Rwenzori mountains shows an inverse metamorphic grade with greenschist facies conditions in the north and amphibolite facies conditions in the south. Early D1 deformation structures are overgrown by cordierite, which in turn grows into D2 deformation, representing the major northwards directed thrusting event. We argue that the inverse metamorphic gradient develops because higher grade rocks are exhumed in the footwall of a crustal scale nappe whereas the exhumation decreases towards the north away from the nappe leading to a decrease in metamorphic grade. The D2 deformation event is followed by a D3 E-W compression, a D4 with the development of steep shear zones with a NNE-SSW and SSE-NNW trend including the large Nyamwamba shear followed by a local D5 retrograde event and D6 brittle inverse faulting. The Paleoproterozoic Buganda-Toro belt is relatively stiff and crosses the NNE-SSW running rift system exactly at the node where the highest peaks of the Rwenzori mountains are situated and where the lake George rift terminates towards the north. Orientation of brittle and ductile fabrics show some similarities indicating that the cross-cutting Buganda-Toro belt influenced rift propagation and brittle fault development within the Rwenzori mountain and that this stiff belt may form part of the reason why the Rwenzori mountains are relatively high within the rift.
Keywords: East African Rift, Basement, Buganda Toro, Inverse Metamorphic Gradient, Microtectonics, Rwenzori mountain
Antiferroquadrupolar Order in the Magnetic Semiconductor TmTe
The physical properties of the antiferroquadrupolar state occurring in TmTe
below TQ=1.8 K have been studied using neutron diffraction in applied magnetic
fields. A field-induced antiferromagnetic component k = (1/2,1/2,1/2) is
observed and, from its magnitude and direction for different orientations of H,
an O(2,2) quadrupole order parameter is inferred. Measurements below TN ~= 0.5
K reveal that the magnetic structure is canted, in agreement with theoretical
predictions for in-plane antiferromagnetism. Complex domain repopulation
effects occur when the field is increased in the ordered phases, with
discontinuities in the superstructure peak intensities above 4 T.Comment: 6 pages, 6 figures, Presented at the International Conference on
Strongly Correlated Electrons with Orbital Degrees of Freedom (ORBITAL 2001),
September 11-14, 2001 (Sendai, JAPAN). To appear in: Journal of the Physical
Society of Japan (2002
Automated simulation of areal bone mineral density assessment in the distal radius from high-resolution peripheral quantitative computed tomography
SummaryAn automated image processing method is presented for simulating areal bone mineral density measures using high-resolution peripheral quantitative computed tomography (HR-pQCT) in the ultra-distal radius. The accuracy of the method is validated against clinical dual X-ray absorptiometry (DXA). This technique represents a useful reference to gauge the utility of novel 3D quantification methods applied to HR-pQCT in multi-center clinical studies and potentially negates the need for separate forearm DXA measurements.IntroductionOsteoporotic status is primarily assessed by measuring areal bone mineral density (aBMD) using 2D dual X-ray absorptiometry (DXA). However, this technique does not sufficiently explain bone strength and fracture risk. High-resolution peripheral quantitative computed tomography (HR-pQCT) has been introduced as a method to quantify 3D bone microstructure and biomechanics. In this study, an automated method is proposed to simulate aBMD measures from HR-pQCT distal radius images.MethodsA total of 117 subject scans were retrospectively analyzed from two clinical bone quality studies. The distal radius was imaged by HR-pQCT and DXA on one of two devices (Hologic or Lunar). Areal BMD was calculated by simulation from HR-pQCT images (aBMD(sim)) and by standard DXA analysis (aBMD(dxa)).ResultsThe reproducibility of the simulation technique was 1.1% (root mean-squared coefficient of variation). HR-pQCT-based aBMD(sim) correlated strongly to aBMD(dxa) (Hologic: R (2) = 0.82, Lunar: R (2) = 0.87), though aBMD(sim) underestimated aBMD(dxa) for both DXA devices (p < 0.0001). Finally, aBMD(sim) predicted aBMD at the proximal femur and lumbar spine with equal power compared to aBMD(dxa).ConclusionThe results demonstrate that aBMD can be simulated from HR-pQCT images of the distal radius. This approach has the potential to serve as a surrogate forearm aBMD measure for clinical HR-pQCT studies when axial bone mineral density values are not required
D^+_s -> pi^+ pi^+ pi^- decay: the 1^3P_0 s anti-s component in scalar-isoscalar mesons
On the basis of data on the decay D^+_s -> pi^+ pi^+ pi^-, which goes
dominantly via the transition D_s -> pi^+ s anti-s, we evaluate the 1^3P_0 s
anti-s components in the scalar-isoscalar resonances f0(980), f0(1300),
f0(1500) and broad state f0(1200-1600)$. The data point to a large s anti-s
component in the f0(980): 40% < s anti-s < 70%. Nearly 30% of the 1^3P_0 s
anti-s component flows to the mass region 1300-1500 MeV being shared by
f0(1300), f0(1500) and broad state f0(1200-1600): the interference of these
states results in a peak near 1400 MeV with the width around 200 MeV.Comment: 17 pages, 4 figures, epsfi
Helimagnon Bands as Universal Spin Excitations of Chiral Magnets
MnSi is a cubic compound with small magnetic anisotropy, which stabilizes a
helimagnetic spin spiral that reduces to a ferromagnetic and antiferromagnetic
state in the long- and short-wavelength limit, respectively. We report a
comprehensive inelastic neutron scattering study of the collective magnetic
excitations in the helimagnetic state of MnSi. In our study we observe a rich
variety of seemingly anomalous excitation spectra, as measured in well over
twenty different locations in reciprocal space. Using a model based on only
three parameters, namely the measured pitch of the helix, the measured
ferromagnetic spin wave stiffness and the amplitude of the signal, as the only
free variable, we can simultaneously account for \textit{all} of the measured
spectra in excellent quantitative agreement with experiment. Our study
identifies the formation of intense, strongly coupled bands of helimagnons as a
universal characteristic of systems with weak chiral interactions.Comment: 8 pages, 4 figures, references updated, introduction updated,
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